So I thought since I have been posting quite a few threads lately, and it will probably continue, that I would create a single thread for all my questions.

First question to start the thread off is this...

So I just wiped my drive. I opened up Gparted and deleted and formated the drive. I then installed Ubuntu onto it, booted into the system, and did some updates. I just randomly checked the Trash and there was a file in it that I deleted before I wiped my system.

How is that possible? Now I know most of my other drives have lost+found folders, and I think one might have had one called Trashed. Do they some how hold that information?

lost+found is the folder like recycle bin in Windows it holds the information about the lost files, but since you format (during installation ?), so its weird that it hold the previous information.
Software center is based on Synaptic manager, so both are same for installing/uninstalling programs.
As for as themes, I think it depends on your own taste

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If I go and try to remove something and get this message. Is it safe to uninstall the application?

I can understand how the "ubuntu-desktop" package looks a little intimidating to uninstall. However, it won't actually affect your system in any practical way. It is merely a meta-package that installs nothing by itself but depends on other packages in the repository. That way, if you choose to install "ubuntu-desktop", every package that is included in your release of Ubuntu by default will be installed. If you uninstall it, the packages it depends on will still be installed unless you explicitly choose to remove them. Software Center is probably telling you to remove it because you selected to remove an application it depends on. That's OK. Remove it.

My screensaver is a black screen. The days when burn-in was a serious concern for most users have long past. Since I'm not at my computer to see the screensaver anyway, there's no point in choosing one. Of course, that's just my preference. I realize that many people still like to have a nice screensaver.